*cough*runabout*cough*
Star Trek has lots of inconsistency. And how can it avoid it, it has lots of material, lots of writers of varying skill and backgrounds, to be inconsistent with. Anything said about it as a generality will have several exceptions. And it also made concessions for various reasons, narrative effect, drama, not wanting to deal with the special effects of landing the ship every episode.
The entire point is that Mass Effect does not have good science and never did. It has lots of technobabble, but not good science. Pointing out Star Trek's science fopaux does not defend Mass Effect against that claim. Spaceships don't become submarines just because it happened in Balance of Terror and Wrath of Khan, either.
It's not a bad thing that Mass Effect has bad science. I just find it silly to pick out beam weapons being weak as somehow worse than the stealth and window problem.